R Notebook

First I want a highly interpolated smoothed data set. Same size bins as usual, but depths by meter, or 1/10 meter. I want the change in flux to be like < 1%.

Then I get adjusted DF for every depth. Then I run remin_shuffle on each depth and extract Cr.

Start with bes. I am assuming I have the usual data. I also have SameGam from GenerateFigures.Rmd, which I think is ready to go.

fine_depths <- seq(from = 1, to = 1500, by = 5)
bds_depths <- unique(bds$depth)

lbbs_FD <- tibble(lb = lb_vec, binsize = binsize_vec)
Expanded_FD <- expand_grid(time = (unique(besE$time)), lb = lb_vec, depth = bds_depths) %>% # undid as.factor of time
  left_join(lbbs_FD, by = "lb")

pt0 <- proc.time()
Pred_FD <- exp(predict(SameGam, Expanded_FD))
pt1 <- proc.time()
pt1 - pt0

   user  system elapsed 
  5.570   0.127   5.697 

Thing_FD <- bind_cols(Expanded_FD, nnparticles = Pred_FD)  %>% mutate(nparticles = nnparticles * binsize) # %>% mutate(time = as.character(time))

Too slow Hey. Here’s an idea. Instead of slicing everything super thin, I could just calculate at the BES locations and like 1m below those locations. And then I look at jumps between each depth and the depth below

space <- 0.01
Expanded_FD_Above <- Expanded_FD %>%
  mutate(depth = depth - space)
Pred_FD_Above <- exp(predict(SameGam, Expanded_FD_Above))
Thing_FD_Above <- bind_cols(Expanded_FD_Above, nnparticles = Pred_FD_Above)  %>% mutate(nparticles = nnparticles * binsize) # %>% mutate(time = as.character(time))

Thing_FD_2 <- bind_cols(Thing_FD, depth_above = Thing_FD_Above$depth, nnparticles_above = Thing_FD_Above$nnparticles, nparticles_above = Thing_FD_Above$nparticles) %>%
  mutate(flux = nparticles * C_f_global * lb ^ ag_global,
         flux_above = nparticles_above * C_f_global * lb ^ ag_global)

Thing_FD_Nested <- Thing_FD_2 %>% group_by(time, depth) %>% 
  nest() %>%
  mutate(spec_only = map(data, ~pull(., nparticles)),
         spec_prev = map(data, ~pull(., nparticles_above))
  )

       DF = smooth_flux_fit - flux_prev,
       #DFP = 1 - DF/flux_prev,  # I was using this for a while.
       DFP = smooth_flux_fit/flux_prev,
       depth_prev = lag(depth),
       DZ = depth - depth_prev,

Thing_FD_FSum <- Thing_FD_2 %>% group_by(time, depth, depth_above) %>% 
  summarize(Flux = sum(flux), Flux_Above = sum(flux_above)) %>%
  mutate(DF = Flux - Flux_Above,
         DFP = Flux/Flux_Above,
         DZ = depth - depth_above)

Thing_FD_FSum

Thing_FD_3 <- left_join(Thing_FD_FSum, Thing_FD_Nested, by = c("time", "depth"))
Thing_FD_3

Thing_FD_4 <- Thing_FD_3 %>%
  mutate(use_DFP = map2_dbl(spec_prev, DFP, optFun, llb = little_lb))
Thing_FD_4

Thing_FD_4 %>% ungroup() %>% summarize(DFPMin = min(DFP), UseDFPMin = min(use_DFP))

I’ve been misspecifying alpha and gamma in the remin model.

#loc_rs <- function(abun_in, DFpct, DeltaZ){remin_shuffle()}
Thing_FD_5 <- Thing_FD_4 %>%
  mutate(Remin = pmap(list(spec_prev, use_DFP, DZ), remin_shuffle)) %>%
  mutate(Cr = map_dbl(Remin, ~.$Cr))
Thing_FD_5

ggplot(Thing_FD_5, aes(y = depth, x = pracma::nthroot(Cr, 5), color = as.factor(time))) + geom_point() + scale_y_reverse(limits = c(1500, 0))

ggplot(Thing_FD_5, aes(y = depth, x = pracma::nthroot(DFP, 5), color = as.factor(time))) + geom_point() + scale_y_reverse(limits = c(1500, 0))

Thing_FD_Slim <- Thing_FD_5 %>% ungroup() %>% select(time, depth, Cr) %>% mutate(time = as.POSIXct(time))
bds_Slim <- bds %>% filter(project == "ETNP") %>% select(profile, time, depth)

bdsCr <- left_join(bds_Slim, Thing_FD_Slim , by = c("time", "depth"))

ggplot(bdsCr, aes(y = depth, x = pracma::nthroot(Cr, 3), color = as.factor(time))) + geom_point() + scale_y_reverse(limits = c(1500, 0)) + scale_x_continuous(limits = c(-0.2, 0.1)) +
  geom_hline(aes(yintercept = PhoticBase), color = "darkgreen") + geom_hline(aes(yintercept = OMZBase), color = "darkblue")